She married Joseph Tilghman in 1970. This marriage ended in the early 1980s, leaving Tilghman with custody of their young daughter (Rebecca) and infant son (Alex). She attributes her successful balancing of a scientific career and caring for her family to organization and focus. Her goal was to not feel guilty while at work or at home, instead focusing on the task at hand.[3]

During postdoctoral studies at the National Institutes of Health, Tilghman made a number of discoveries while a member of the team which cloned the first mammalian gene. She went on to demonstrate that the globin gene was spliced, a finding that helped confirm some of the revolutionary theories then emerging about gene behavior. She continued to make scientific breakthroughs as an independent investigator at the Institute for Cancer Research in Philadelphia and as an adjunct associate professor of Human Genetics at University of Pennsylvania.[citation needed]

Tilghman went to Princeton University in 1986 as the Howard A. Prior Professor of the Life Sciences. Two years later, she also joined the Howard Hughes Medical Institute as an investigator. She was a leader in the use of mice to understand the behavior of genes by researching the effect of gene insertion in embryonic cells.[citation needed]

In 1998, she took on additional responsibilities as the founding director of Princeton's multi-disciplinary Lewis-Sigler Institute for Integrative Genomics, while continuing to study how male and female genomes are packaged and the consequences of the differences for regulating embryo growth.[citation needed]

Tilghman succeeded Harold Tafler Shapiro and became the 19th President of Princeton University in 2001. She was elected Princeton's first woman president on May 5, 2001, and assumed office on June 15, 2001. Under her administration, the University built a sixth residential college, named in honor of alumna Meg Whitman, to accommodate an 11 percent expansion of the undergraduate student body (an increase of some 500 students), as recommended by a special committee of the Board of Trustees chaired by Paul M. Wythes. Recently, however, Tilghman announced that she will be stepping down from her presidency in June 2013.[4]

The establishment of Whitman College, together with the reconstruction of Butler College, accompanied a significant reconfiguration of Princeton's residential college system, which now incorporates upperclassmen as well as freshmen and sophomores, providing new residential options and increasing opportunities for social interaction across the student body. In addition, an effort has been made to strengthen the relationship between the university and Princeton's independent eating clubs, where most upperclassmen take their meals, with the goal of enhancing the undergraduate experience of all students. In 2009, she appointed a committee chaired by Nannerl O. Keohane to review undergraduate women's leadership at Princeton.[5]

Tilghman has presided over a number of academic initiatives, including the creation of a Center for African American Studies, the Lewis Center for the Arts (after alumnus Peter B. Lewis), the Princeton Neuroscience Institute and the Andlinger Center for Energy and the Environment (after alumnus Gerhard R. Andlinger). Along with the renewal of the Department of Chemistry, these steps have both capitalized on Princeton's existing strengths and broken new ground, ensuring that the university will, in Tilghman's words, continue "to make the world a better place through the power of the mind and the imagination." [6]

More broadly, Tilghman's presidency has placed an emphasis on increasing the diversity of Princeton's faculty and students; widening access to the university through improvements to its generous financial aid program and the elimination of admission through "early decision"; fostering a multidisciplinary approach to teaching and research; and strengthening the university's international perspective through a wide range of initiatives – from the Global Scholars Program, which brings international scholars to campus on a recurring basis, to the Bridge Year Program, which gives incoming freshmen an opportunity to defer their studies for a year in order to devote themselves to public service overseas.

For Tilghman, Princeton has two essential missions. "One is to ensure that our doors are open as wide as possible to every talented student in the world who is capable of doing the hard work we ask of them. And that means maintaining our commitment to financial aid, which is the tool – the critical tool – to get those students to Princeton. And the second thing is that we must address the most critical issues, and push back the frontiers of knowledge, and not just in science and technology, but in social policy, and in public policy, and in understanding the nature of the human condition." [7]

Tilghman also signed on to the Ivy League-wide Seven-week athletic moratorium, in which intercollegiate athletes were enjoined from taking part in supervised practices and other obligatory athletic activities for seven weeks during the academic year in order to encourage them to participate in other activities. Supporters of the proposal pointed to studies by former Princeton president William G. Bowen, whose book The Game of Life described the widespread academic underperformance of college athletes. Detractors claimed that it represented an encroachment on students' freedom to use their time as they saw fit.

While Tilghman has disquieted some alumni by promoting a more diverse university community, establishing a single admission process, and broadening the range of residential and dining options available to students, she has also found strong support for these actions and the vision that underpins them.

On September 21, 2012, Shirley informed the Princeton Board of Trustees that she planned to step down as the 19th President of Princeton University at the end of the 2012 academic year.

Tilghman has served as a member of the board of directors of Google since October 2005. As compensation for joining the board, she received 6,000 shares of stock that by 2005 were worth in excess of her Princeton compensation package that by 2003 had reached $533,057.[17]

"What made it truly thrilling was that the genes were organized in a way that was totally unexpected. So nature took us by surprise."[19]

"There are 25 years of good social science that demonstrate the many cultural practices that act collectively to discourage women from entering and continuing careers in science and engineering. The research is overwhelming, and it is there for anybody to see. On the other hand, the data that would suggest there are innate differences in the abilities of men and women to succeed in the natural sciences are nonexistent."[20]

Tilghman, Shirley, et al. (1994) The Funding of Young Investigators in the Biological and Biomedical Sciences. ISBN 0-309-05077-4

Tilghman, Shirley and National Research Council Committee on Dimensions, Causes, and Implications of Recent Trends in the Careers of Life Scientists (1998) Trends in the Careers of Life Scientists. Molecular Biology of the Cell Vol. 9, 3007–3015